''
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14136 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -433,14 +433,14 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
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package</A>.
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR ALIGN="center"><TD ><A HREF = "fix_adapt_fep.html">adapt/fep</A></TD><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_ave_spatial_sphere.html">ave/spatial/sphere</A></TD><TD ><A HREF = "fix_drude.html">drude</A></TD><TD ><A HREF = "fix_drude_transform.html">drude/transform/direct</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_drude_transform.html">drude/transform/reverse</A></TD><TD ><A HREF = "fix_colvars.html">colvars</A></TD><TD ><A HREF = "fix_gle.html">gle</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_ipi.html">ipi</A></TD><TD ><A HREF = "fix_langevin_drude.html">langevin/drude</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_lb_fluid.html">lb/fluid</A></TD><TD ><A HREF = "fix_lb_momentum.html">lb/momentum</A></TD><TD ><A HREF = "fix_lb_pc.html">lb/pc</A></TD><TD ><A HREF = "fix_lb_rigid_pc_sphere.html">lb/rigid/pc/sphere</A></TD><TD ><A HREF = "fix_lb_viscous.html">lb/viscous</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_meso.html">meso</A></TD><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_phonon.html">phonon</A></TD><TD ><A HREF = "fix_pimd.html">pimd</A></TD><TD ><A HREF = "fix_qbmsst.html">qbmsst</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_qtb.html">qtb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_saed_vtk.html">saed/vtk</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_smd_adjust_dt.html">smd/adjust/dt</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_smd_integrate_tlsph.html">smd/integrate/tlsph</A></TD><TD ><A HREF = "fix_smd_integrate_ulsph.html">smd/integrate/ulsph</A></TD><TD ><A HREF = "fix_smd_move_triangulated_surface.html">smd/move/triangulated/surface</A></TD><TD ><A HREF = "fix_smd_setvel.html">smd/setvel</A></TD><TD ><A HREF = "fix_smd_tlsph_reference_configuration.html">smd/tlsph/reference/configuration</A></TD><TD ><A HREF = "fix_smd_wall_surface.html">smd/wall/surface</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A></TD><TD ><A HREF = "fix_ttm.html">ttm/mod</A>
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<TR ALIGN="center"><TD ><A HREF = "fix_adapt_fep.html">adapt/fep</A></TD><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_ave_correlate_long.html">ave/correlate/long</A></TD><TD ><A HREF = "fix_ave_spatial_sphere.html">ave/spatial/sphere</A></TD><TD ><A HREF = "fix_drude.html">drude</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_drude_transform.html">drude/transform/direct</A></TD><TD ><A HREF = "fix_drude_transform.html">drude/transform/reverse</A></TD><TD ><A HREF = "fix_colvars.html">colvars</A></TD><TD ><A HREF = "fix_gle.html">gle</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_ipi.html">ipi</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_langevin_drude.html">langevin/drude</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_lb_fluid.html">lb/fluid</A></TD><TD ><A HREF = "fix_lb_momentum.html">lb/momentum</A></TD><TD ><A HREF = "fix_lb_pc.html">lb/pc</A></TD><TD ><A HREF = "fix_lb_rigid_pc_sphere.html">lb/rigid/pc/sphere</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_lb_viscous.html">lb/viscous</A></TD><TD ><A HREF = "fix_meso.html">meso</A></TD><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_phonon.html">phonon</A></TD><TD ><A HREF = "fix_pimd.html">pimd</A></TD><TD ><A HREF = "fix_qbmsst.html">qbmsst</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD><TD ><A HREF = "fix_qtb.html">qtb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_saed_vtk.html">saed/vtk</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_smd_adjust_dt.html">smd/adjust/dt</A></TD><TD ><A HREF = "fix_smd_integrate_tlsph.html">smd/integrate/tlsph</A></TD><TD ><A HREF = "fix_smd_integrate_ulsph.html">smd/integrate/ulsph</A></TD><TD ><A HREF = "fix_smd_move_triangulated_surface.html">smd/move/triangulated/surface</A></TD><TD ><A HREF = "fix_smd_setvel.html">smd/setvel</A></TD><TD ><A HREF = "fix_smd_tlsph_reference_configuration.html">smd/tlsph/reference/configuration</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_smd_wall_surface.html">smd/wall/surface</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A></TD><TD ><A HREF = "fix_ttm.html">ttm/mod</A>
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</TD></TR></TABLE></DIV>
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<HR>
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@ -23,7 +23,7 @@
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<LI>Nrepeat = # of correlation time windows to accumulate
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<LI>Nfreq = calculate tine window averages every this many timesteps
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<LI>Nfreq = calculate time window averages every this many timesteps
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<LI>one or more input values can be listed
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@ -80,7 +80,10 @@ and average the correlation data over longer timescales. The
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resulting correlation values can be time integrated by
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<A HREF = "variable.html">variables</A> or used by other <A HREF = "Section_howto.html#howto_15">output
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commands</A> such as <A HREF = "thermo_style.html">thermo_style
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custom</A>, and can also be written to a file.
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custom</A>, and can also be written to a file. See the
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<A HREF = "fix_ave_correlate_long.html">fix ave/correlate/long</A> command for an
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alternate method for computing correlation functions efficiently over
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very long time windows.
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</P>
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<P>The group specified with this command is ignored. However, note that
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specified values may represent calculations performed by computes and
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@ -337,7 +340,8 @@ minimization</A>.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "fix_ave_atom.html">fix
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<P><A HREF = "fix_ave_correlate_long.html">fix ave/correlate/long</A>,
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<A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "fix_ave_atom.html">fix
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ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>,
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<A HREF = "fix_ave_histo.html">fix ave/histo</A>, <A HREF = "variable.html">variable</A>
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</P>
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159
doc/doc2/fix_ave_correlate_long.html
Normal file
159
doc/doc2/fix_ave_correlate_long.html
Normal file
@ -0,0 +1,159 @@
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
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<HR>
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<H3>fix ave/correlate/long command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID ave/correlate/long Nevery Nfreq value1 value2 ... keyword args ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>ave/correlate/long = style name of this fix command
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<LI>Nevery = use input values every this many timesteps
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<LI>Nfreq = save state of the time correlation functions every this many timesteps
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<LI>one or more input values can be listed
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<LI>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
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<PRE> c_ID = global scalar calculated by a compute with ID
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c_ID[I] = Ith component of global vector calculated by a compute with ID
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f_ID = global scalar calculated by a fix with ID
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f_ID[I] = Ith component of global vector calculated by a fix with ID
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v_name = global value calculated by an equal-style variable with name
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</PRE>
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<LI>zero or more keyword/arg pairs may be appended
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<LI>keyword = <I>type</I> or <I>start</I> or <I>file</I> or <I>overwrite</I> or <I>title1</I> or <I>title2</I> or <I>ncorr</I> or <I>p</I> or <I>m</I>
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<PRE> <I>type</I> arg = <I>auto</I> or <I>upper</I> or <I>lower</I> or <I>auto/upper</I> or <I>auto/lower</I> or <I>full</I>
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auto = correlate each value with itself
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upper = correlate each value with each succeeding value
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lower = correlate each value with each preceding value
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auto/upper = auto + upper
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auto/lower = auto + lower
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full = correlate each value with every other value, including itself = auto + upper + lower
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<I>start</I> args = Nstart
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Nstart = start accumulating correlations on this timestep
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<I>file</I> arg = filename
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filename = name of file to output correlation data to
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<I>overwrite</I> arg = none = overwrite output file with only latest output
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<I>title1</I> arg = string
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string = text to print as 1st line of output file
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<I>title2</I> arg = string
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string = text to print as 2nd line of output file
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<I>ncorr</I> arg = Ncorrelators
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Ncorrelators = number of correlators to store
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<I>nlen</I> args = Nlen
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Nlen = length of each correlator
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<I>ncount</I> args = Ncount
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Ncount = number of values over which succesive correlators are averaged
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
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fix 1 all ave/correlate/long 1 10000 &
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c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
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type upper title1 "My correlation data" nlen 15 ncount 3
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This fix is similar in spirit and syntax to the <A HREF = "fix_ave_correlate.html">fix
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ave/correlate</A>. However, this fix allows the
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efficient calculation of time correlation functions on the fly over
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extremely long time windows without too much CPU overhead, using a
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multiple-tau method <A HREF = "#Ramirez">(Ramirez)</A> that decreases the resolution
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of the stored correlation function with time.
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</P>
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<P>The group specified with this command is ignored. However, note that
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specified values may represent calculations performed by computes and
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fixes which store their own "group" definitions.
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</P>
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<P>Each listed value can be the result of a compute or fix or the
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evaluation of an equal-style variable. See the <A HREF = "fix_ave_correlate.html">fix
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ave/correlate</A> doc page for details.
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</P>
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<P>The <I>Nevery</I> and <I>Nfreq</I> arguments specify on what timesteps the input
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values will be used to calculate correlation data, and the frequency
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with which the time correlation functions will be output to a file.
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Note that there is no <I>Nrepeat</I> argument, unlike the <A HREF = "fix_ave_correlate.html">fix
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ave/correlate</A> command.
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</P>
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<P>The optional keywords <I>ncorr</I>, <I>nlen</I>, and <I>ncount</I> are unique to this
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command and determine the number of correlation points calculated and
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the memory and CPU overhead used by this calculation. <I>Nlen</I> and
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<I>ncount</I> determine the amount of averaging done at longer correlation
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times. The default values <I>nlen=16</I>, <I>ncount=2</I> ensure that the
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systematic error of the multiple-tau correlator is always below the
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level of the statistical error of a typical simulation (which depends
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on the ensemble size and the simulation length).
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</P>
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<P>The maximum correlation time (in time steps) that can be reached is
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given by the formula (nlen-1) * ncount^(ncorr-1). Longer correlation
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times are discarded and not calculated. With the default values of
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the parameters (ncorr=20, nlen=16 and ncount=2), this corresponds to
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7864320 time steps. If longer correlation times are needed, the value
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of ncorr should be increased. Using nlen=16 and ncount=2, with
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ncorr=30, the maximum number of steps that can be correlated is
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80530636808. If ncorr=40, correlation times in excess of 8e12 time
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steps can be calculated.
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</P>
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<P>The total memory needed for each correlation pair is roughly
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4*ncorr*nlen*8 bytes. With the default values of the parameters, this
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corresponds to about 10 KB.
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</P>
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<P>For the meaning of the additional optional keywords, see the <A HREF = "fix_ave_correlate.html">fix
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ave/correlate</A> doc page.
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</P>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>Since this fix in intended for the calculation of time correlation
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functions over very long MD simulations, the information about this
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fix is written automatically to binary restart files, so that the time
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correlation calculation can continue in subsequent simulations. None
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of the fix_modify options are relevant to this fix.
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</P>
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<P>No parameter of this fix can be used with the start/stop keywords of
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the run command. This fix is not invoked during energy minimization.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>This compute is part of the USER-MISC package. It is only enabled if
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LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_ave_correlate.html">fix ave/correlate</A>
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</P>
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<P><B>Default:</B> none
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</P>
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<P>The option defaults for keywords that are also keywords for the <A HREF = "fix_ave_correlate.html">fix
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ave/correlate</A> command are as follows: type =
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auto, start = 0, no file output, title 1,2 = strings as described on
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the <A HREF = "fix_ave_correlate.html">fix ave/correlate</A> doc page.
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</P>
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<P>The option defaults for keywords unique to this command are as
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follows: ncorr=20, nlen=16, ncount=2.
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</P>
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<HR>
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<A NAME = "Ramirez"></A>
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<P><B>(Ramirez)</B> J. Ramirez, S.K. Sukumaran, B. Vorselaars and
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A.E. Likhtman, J. Chem. Phys. 133, 154103 (2010).
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</P>
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</HTML>
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Reference in New Issue
Block a user